Journal Article The development and application of bioinformatics core competencies to improve bioinformatics training and education 2018 • PLoS Computational Biology • 14(2): Mulder N, Schwartz R, Brazas MD, Brooksbank C, Gaeta B, Morgan SL, Pauley MA, Rosenwald A, Rustici G, Sierk M, Warnow T, Welch L
Journal Article The evolution of single cell-derived colorectal cancer cell lines is dominated by the continued selection of tumor-specific genomic imbalances, despite random chromosomal instability 2018 • Carcinogenesis • 39(8):993-1157 Wangsa D, Braun R, Schiefer M, Gertz EM, Bronder D, Quintanilla I, Padilla-Nash HM, Torres I, Hunn C, Warner L, Buishand FO, Hu Y, Hirsch D, Gaiser T, Camps J, Schwartz R, Schaffer AA, Heselmeyer-Haddad K, Ried T
Conference Tumor Copy Number Data Deconvolution Integrating Bulk and Single-cell Sequencing Data 2018 • IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences Lei H, Lyu B, Gertz EM, Schaffer AA, Schwartz R
Conference Tumor Copy Number Data Deconvolution Integrating Bulk and Single-cell Sequencing Data 2018 1-1 Lei H, Lyu B, Gertz EM, Schaffer AA, Schwartz R
Conference Abstract 2908: Single-cell genetic analysis of ductal carcinoma in situ with and without synchronous invasive breast cancer by multiplex FISH delineates specific patterns of tumor clonality and heterogeneity 2017 • Cancer Research • 77(13_Supplement):2908-2908 Torres IM, Hernandez L, Tzeng J, Schwartz R, Schaffer A, Gertz E, Brower S, Sanchez M, Auer G, Heselmeyer-Haddad K, Thomas R
Conference Abstract 4387: The clonal composition of colorectal cancer cell lines is defined by the maintenance of specific genomic imbalances, not by ongoing chromosomal instability 2017 • Cancer Research • 77(13_Supplement):4387-4387 Wangsa D, Schiefer M, Bronder D, Padilla-Nash H, Torres I, Warner L, Hu Y, Gertz EM, Schwartz R, Schäffer AA, Hirsch D, Gaiser T, Meyer R, Camps J, Heselmeyer-Haddad K, Ried T
Journal Article Automated deconvolution of structured mixtures from heterogeneous tumor genomic data 2017 • PLoS Computational Biology • 13(10): Roman T, Xie L, Schwartz R
Journal Article Derivative-Free Optimization of Rate Parameters of Capsid Assembly Models from Bulk in Vitro Data 2017 • IEEE/ACM Transactions on Computational Biology and Bioinformatics • 14(4):844-855 Xie L, Smith GR, Schwartz R
Journal Article Quantitative computational models of molecular self-assembly in systems biology 2017 • Physical Biology • 14(3): Thomas M, Schwartz R
Journal Article The evolution of tumour phylogenetics: principles and practice 2017 • Nature Reviews Genetics • 18(4):213-229 Schwartz R, Schaffer AA
Journal Article Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee) 2016 • PLoS Computational Biology • 12(5): Welch L, Brooksbank C, Schwartz R, Morgan SL, Gaeta B, Kilpatrick AM, Mietchen D, Moore BL, Mulder N, Pauley M, Pearson W, Radivojac P, Rosenberg N, Rosenwald A, Rustici G, Warnow T
Preprint Automated deconvolution of structured mixtures from bulk tumor genomic data 2016 Roman T, Xie L, Schwartz R
Journal Article Classifying the Progression of Ductal Carcinoma from Single-Cell Sampled Data via Integer Linear Programming: A Case Study 2016 • IEEE/ACM Transactions on Computational Biology and Bioinformatics • 13(4):643-655 Catanzaro D, Shackney SE, Schaffer AA, Schwartz R
Conference Computationally resolving heterogeneity in mixed genomic samples 2016 • IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences Schwartz R
Journal Article FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe 2016 • PLoS ONE • 11(6): Gertz EM, Chowdhury SA, Lee W-J, Wangsa D, Heselmeyer-Haddad K, Ried T, Schwartz R, Schaffer AA
Journal Article Medoidshift clustering applied to genomic bulk tumor data 2016 • BMC Genomics • 17: Roman T, Xie L, Schwartz R
Journal Article Modeling Effects of RNA on Capsid Assembly Pathways via Coarse-Grained Stochastic Simulation 2016 • PLoS ONE • 11(5): Smith GR, Xie L, Schwartz R
Journal Article Phylogenetic analysis of multiple FISH markers in oral tongue squamous cell carcinoma suggests that a diverse distribution of copy number changes is associated with poor prognosis 2016 • International Journal of Cancer • 138(1):98-109 Wangsa D, Chowdhury SA, Ryott M, Gertz EM, Elmberger G, Auer G, Lundqvist EA, Kueffer S, Stroebel P, Schaeffer AA, Schwartz R, Munck-Wikland E, Ried T, Heselmeyer-Haddad K
Journal Article Reference-free inference of tumor phylogenies from single-cell sequencing data (vol 16, S7, 2015) 2016 • BMC Genomics • 17: Subramanian A, Schwartz R
Journal Article A simplicial complex-based approach to unmixing tumor progression data 2015 • BMC Bioinformatics • 16: Roman T, Nayyeri A, Fasy BT, Schwartz R
Journal Article Applying Derivative-Free Optimization to Fit Kinetic Parameters of Viral Capsid Self-Assembly Models from Multi-Source Bulk in vitro Data 2015 • Biophysical Journal • 108(2):470A-471A Xie L, Smith G, Schwartz R
Journal Article Computationally Projecting the Influence of Nucleic Acid on Pathways of Nucleation-Limited Virus Capsid Assembly 2015 • Biophysical Journal • 108(2):319A-319A Smith GR, Xie L, Schwartz R
Journal Article Identification of Novel Mutations by Exome Sequencing in African American Colorectal Cancer Patients 2015 • Cancer • 121(1):34-42 Ashktorab H, Daremipouran M, Devaney J, Varma S, Rahi H, Lee E, Shokrani B, Schwartz R, Nickerson ML, Brim H
Conference Improved deconvolution of heterogeneous tumor data to reconstruct clonal evolution from bulk genomic samples 2015 • Cancer Research • 75: Roman T, Schwartz R
Journal Article Inferring models of multiscale copy number evolution for single-tumor phylogenetics 2015 • Bioinformatics • 31(12):258-267 Chowdhury SA, Gertz EM, Wangsa D, Heselmeyer-Haddad K, Ried T, Schaeffer AA, Schwartz R
